CAP 5510 & CGS 5166: Fall 2018
Bioinformatics Course Homepage
MW 5:00 - 6:15, ECS 138

• Nov 25: Presentation Order:
  
  • Monday, Nov 26: BV Microbiome (Daniel, Makella); GEO Chip (Cesar, Maurell, Mona); Soil Provenance (Deidra, Farzana, Noelle, Vitalii); Primers (Alexander, Eric);
  • Wednesday, Nov 28: NR Peptides (Mallory, Muhammad); Proteogenomics (Usman); Volatilome (Chantrell, Kevin, Kierstin)
• Nov 25: Project Final Reports are due by 11:59 PM on Sunday, Dec 2. To know what to include in your final report: Click here.
• Nov 07: No class today. Please check this page for further announcements.
• Sep 30: There are several teams still looking for a possible teammate. If you are still not part of a team or you need one more team member, email me immediately with your plan for a project (if you have one).
• Sep 26: Read about HW3 below. It involves writing a brief proposal for a semester project for this class. Some instructions and possibe ideas for a project can be found here.
• Sep 19: You need not submit the weekly blurbs after this week.
• Aug 29: You have some guest lectures coming up. You will have lectures from Camilo Valdes (about 10 years of real-world Bioinfoematics experience), Prof. Kalai Mathee (Professor, College of Medicine, FIU), and Arpit Mehta (about 10 years of real-world Bioinformatics experience).
• Aug 29: For your class project, an ideal group must have 3 members, 2 from CS and 1 from the Life sciences. Please get it cleared from me if you intend to deviate from this ideal.
• Aug 29: Clarifications on weekly blurbs. Write a brief note/paragraph on anything of interest you may have read/seen/heard on popular media or scientific press/websites. The topic must pertian broadly to Bioinformatics and the Life Sciences. In the blurb, briefly describe what you learnt and why you think it is interesting. Do not cut and paste. Use your own words as much as possible.
• Aug 29: Hoemwork #2 is now ready. See bwlo for details It is due Sep 12 by email. E-mail all homework to cap5510-f18@cs.fiu.edu
• Aug 27: E-mail all homework to cap5510-f18@cs.fiu.edu or to cap5166-f18@cs.fiu.edu
  
• Aug 22: We will do a survey in order to use an educational App called Momentos. Before the survey, please read the following Consent Form. Note that I will not see the results of the survey until the semester ends.
• Aug 20: Homework 1 is ready and is due Aug 27.

• For CS Majors: CAP 5510
• For NON-CS Students: CGS 5166

• Nov 21: Exam Review [Review]
• Nov 07: Lecs 22 [pdf]; Lecture by Camilo Valdes: Structure
• Oct 29, Oct 31, Nov 05: Lecs 19, 20, 21 [pdf]; Lectures by Camilo Valdes: Tree of Life and Phylogeny;
• Oct 24: Lec 18 [pdf]; GWAS
• Oct 22: Lec 17 [pdf]; Machine Learning; Neural Networks
• Oct 15: Lec 16 [pdf]; Machine Learning; SVMs
• Oct 10: Lec 15 [pdf]; Perl and Python; Also try out the Python notebook bioPy1.ipynb containing some basic BioPython commands. Note that you need to install Anaconda before working with BioPython.
• Oct 08: Lec 14 [pdf]; Proteins and Proteomics
• Oct 03: Lec 13 [pdf]; Clustering
• Oct 01: Lec 12 [pdf]; Hidden Markov Models (HMMs)
• Sep 26: Lec 11 [pdf]; Assmebly of NGS Data
• Sep 24: Lec 10 [pdf]; Next-Generation Sequencing (NGS)
• Sep 19: Lec 9 [pdf]; Next-Generation Sequencing (NGS)
• Sep 17: Lec 8 [pdf]; PCR, Gel Electrophoresis, and Sanger Sequencing
• Sep 12: Lec 7 [pdf]; Guest Lecture by Arpit Mehta, PhD student and Lead Bioinformaticist, Miami Cancer Institute.
• Sep 10: Lec 6 [pdf]; Guest Lecture by Prof. Kalai Mathee, Professor in Molecular Microbiology, College of Medicine, FIU.
• Sep 5: Lec 5 [pdf]; Guest Lecture by Camilo Valdes, PhD student, and over 10 years of experience in Bioinformatics
• Sep 3: Memorial Holiday
• Aug 29: Lec 4 [StatisticalPreliminaries]; [ pdf]
• Aug 27: Lec 3 [pdf]
• Aug 22: Lec 2 [pdf] [Mol Biol Preliminaries; Public Databases; Sequence Alignment]; [Lecture Slides by Pevsner pdf]
• Aug 20: Lec 1 [pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from Pevsner); Also see section on "Additional Reading" below]; [Statistical Preliminaries]; [MIT Lectures on Computational Biology]

• HW 1 Due Aug 27, at the start of class.
• HW 2 Due Sep 12, at the start of class by email.
• HW 3 Due Oct 8, at start of class. For this homework, submit a brief paragraph describing your semester project. Some instructions and possibe ideas for a project can be found here.
• HW 4 This is optional for CGS 5166 students. Install Anaconda a software distribution package that provides an environment for doing Data Science using Python and R. The Jupyter installation inside Anaconda allows for the use of Python Notebooks. Next install BioPython by following instructions here. You are now ready to try out BioPython.
• HW 5 Due Oct 29, at the start of class.

• Bioinformatics and Functional Genomics, by Jonathan Pevsner, Wiley-Blackwell Press, 2009, 3rd Edition, ISBN-13: 978-1118581780; ISBN-10: 1118581784

• Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.
• Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• Understanding Bioinformatics, by Zvelebil & Baum, ISBN: 0-815-34024-9.
• Introduction to Bioinformatics, by Arthur M. Lesk, 3rd Edition, Oxford University Press, 2008.

• News: Genome News Network. Online magazine covering important developments in genomics research.
• Popular: Virtual Cell Animation Collection. Find some great animations here, especially ones on Transcription and Regulated Transcription.
• Popular: Time, Love, Memory, by Jonathan Weiner, 1999.
• Useful Blurbs: What's a Genome (and also Chromosome, Gene, DNA, Sequencing, genome map, genome variations), by Sarah E. DeWeedt, 2003.
• Guide to Sequenced Genomes